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Crystal structure of Y116T/I16A double mutant of 5-hydroxyisourate hydrolase in complex with T4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IWU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 278 0.1M HEPES, 20% PEG 10000, pH 7.5, VAPOR DIFFUSION, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.27 45.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.771 α = 90 b = 103.462 β = 109.47 c = 53.49 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD SI(111) and Pt coated mirrors in KB geometry 2009-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 51.73 99 0.054 9.5 2.5 33889 33889
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.95 2.06 94.3 0.458 2.1 2.3 4721
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3IWU 1.95 51.73 33863 33863 1717 98.97 0.22489 0.22489 0.22227 0.2422 0.27116 0.2913 RANDOM 43.866
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 4.77 2.88 -1.58 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.252 r_dihedral_angle_4_deg 24.084 r_dihedral_angle_3_deg 15.768 r_dihedral_angle_1_deg 6.697 r_scangle_it 3.761 r_scbond_it 2.554 r_angle_refined_deg 1.907 r_mcangle_it 1.477 r_mcbond_it 0.903 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.252 r_dihedral_angle_4_deg 24.084 r_dihedral_angle_3_deg 15.768 r_dihedral_angle_1_deg 6.697 r_scangle_it 3.761 r_scbond_it 2.554 r_angle_refined_deg 1.907 r_mcangle_it 1.477 r_mcbond_it 0.903 r_chiral_restr 0.129 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3579 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 10
Software Software Software Name Purpose ADSC data collection MLPHARE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling